Proteins with intrinsically disordered regions (IDRs) are common among eukaryotes. Many IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported by computational predictors, but to date, only one tool that predicts...
There is great interest to develop artificial intelligence-based protein-ligand binding affinity models due to their immense applications in drug discovery. In this paper, PointNet and PointTransformer, two pointwise multi-layer perceptrons have been...
Accurate identification of transcription factor binding sites is of great significance in understanding gene expression, biological development and drug design. Although a variety of methods based on deep-learning models and large-scale data have bee...
The cooperativity of transcription factors (TFs) is a widespread phenomenon in the gene regulation system. However, the interaction patterns between TF binding motifs remain elusive. The recent high-throughput assays, CAP-SELEX, have identified over ...
Binding free energy estimation of drug candidates to their biomolecular target is one of the best quantitative estimators in computer-aided drug discovery. Accurate binding free energy estimation is still a challengeable task even after decades of re...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2022
Drug-target residence time, the duration of binding at a given protein target, has been shown in some protein families to be more significant for conferring efficacy than binding affinity. To carry out efficient optimization of residence time in drug...
SUMMARY: The ability to unveil binding patterns in peptide sets has important applications in several biomedical areas, including the development of vaccines. We present an open-source tool, CNN-PepPred, that uses convolutional neural networks to dis...
The accumulation of large epigenomics data consortiums provides us with the opportunity to extrapolate existing knowledge to new cell types and conditions. We propose Epitome, a deep neural network that learns similarities of chromatin accessibility ...
Deep residual learning has shown great success in protein contact prediction. In this study, a new deep residual learning-based protein contact prediction model was developed. Comparing with previous models, a new type of residual block hybridizing 1...
Transcription factors (TFs) are essential proteins in regulating the spatiotemporal expression of genes. It is crucial to infer the potential transcription factor binding sites (TFBSs) with high resolution to promote biology and realize precision med...